As a more precise method IMHO, get some solder and use that instead of clay. The biggest we can get here is .062 (1.58mm) and that works well. Run the piston up close to TDC but not all the way, unroll 5 or 6 inches (sorry) put a slight bend in it, and feed it in the plug hole. You'll fell it slide along the piston done and then hit the cylinder wall. Practice if you need to. Once you're confident it's touching the cylinder wall, run the piston up past TDC. You'll feel it hit the solder. Pull the solder out and you'll see it flattened. Measure that section. You can cut that small flattened section off and do the same measurement again at four different points around the circumference of the head. The measurements will vary as probably already discussed in this thread due to mis-alignment issues with the engines design, but don't worry about that yet, you're not building a race motor here. You'll get a good feel for the average squish clearance this way and you can make changes accordingly. If the 1.58 gauge solder is not big enough to be squished by the test then using your clay measurements as a reference, take a small cut or cuts off the head and check clearance again with the solder method until you get can get a measurable squish in the solder. Fine tune the clearance from there.
With a stock chamber design, set it at 1mm and don't worry about MSV or redesigning anything. We did not for decades and stock ported street motors ran just fine set up that way. If you want to further refine it, that is a valuable aspect to refine and there is probably freeware out there now to help you do so. Way back when I bought that and several other programs from TSR, now gone, that greatly aided in designing cylinders and heads. I have not fired those up in years, probably won't even run on current windows machines. I wonder where those are? I should try and run them for fun.